Pan cancer quantitative analysis of differential expression of HOX genes compared with correlated healthy tissues

HOX genes are a subset of homeotic genes that control the body plan of an embryo along the head-to-tail axis. The human HOX genes are organized in four genomic clusters. They encode transcription factors that function as critical master regulators during embryogenesis. Multiple reports have shown that mis-regulation of their expression plays key roles in the development of cancers. The expression levels of HOX genes in cancers tend to differ based on tissue and tumor type. Here, we performed a comprehensive analysis comparing HOX gene expression in different cancer types and matched healthy tissues. We identified and quantified differential expression patterns that confirmed previously identified expression changes and highlighted new differential expression signatures, which are in line with patient survival data. Furthermore, we identified HOX genes whose expression levels change together in multiple cancer types. This comprehensive and quantitative analysis provides a global picture of HOX genes’ differential expression patterns in different cancer types. Importantly, the quantitative characterization of specific differentially expressed HOX genes highlights novel prognostic markers, which can be used to discriminate between healthy and tumor tissues.